To utilise effectively the growing number of verified genes that mediate an organism's ability to cause disease and / or to trigger host responses, we have developed PHI-base.

This is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from fungal and Oomycete pathogens which infect animal, plant and fungal hosts. PHI-base is the first on-line resource devoted to the identification and presentation of information on fungal and Oomycete pathogenicity genes and their host interactions. As such, PHI-base is a strong valuable resource for the discovery of candidate targets in medically and agronomically important fungal and Oomycete pathogens for intervention with synthetic chemistries and natural products.

Each entry in PHI-base is curated by domain experts and supported by strong experimental evidence (gene disruption experiments) as well as literature references in which the experiments are described. Each gene in PHI-base is presented with its nucleotide and deduced amino acid sequence as well as a detailed structured description of the predicted protein's function during the host infection process. To facilitate data interoperability, we have annotated genes using controlled vocabularies (Gene Ontology terms, EC Numbers, etc.), and provide links to other external data sources (for example, NCBI taxonomy, EMBL and COGEME).

PUBLICATIONS ON PHI-BASE

Baldwin, T.K., Winnenburg, R., Urban, M., Rawlings, C., Köhler, J. and Hammond-Kosack, K.E. 2006. The Pathogen-Host Interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity. Mol Plant Microbe Interact. 19(12):1451-62
PubMed:17153929

Winnenburg, R., Baldwin, T.K., Urban, M., Rawlings, C., Köhler, J. and Hammond-Kosack, K.E. 2006. PHI-base: a new database for pathogen host interactions. Nucleic Acids Research. 34(Database issue):D459-D464
PubMed:16381911


ORAL PRESENTATIONS ON PHI-BASE

2006

Thomas K. Baldwin, Rainer Winnenburg, Martin Urban, Chris Rawlings, Jacob Köhler and Kim E. Hammond-Kosack
PHI-base: A database of experimentally verified pathogenicity, virulence and effector genes in fungal and Oomycete pathogens of animals and plants
8th European Conference on Fungal Genetics in the Symposium “Mechanisms of human pathogenesis” 8th – 11th April 2006, Vienna, Austria
Online:Conference Presentation

2005

Thomas Baldwin, Rainer Winnenburg, Jacob Köhler, Martin Urban and Kim Hammond-Kosack
Bioinformatic and molecular genetic tools for identifying genes involved in pathogenicity
XVI Molecular Biology of Plant Pathogens meeting, Ambleside 19-21th September 2005
ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Sant Feliu de Guixols, Spain. November 2005
(Oral and poster presentations)

Thomas Baldwin, Rainer Winnenburg, Jacob Köhler, Martin Urban and Kim Hammond-Kosack
Bioinformatic and molecular genetic tools for identifying genes involved in the pathogenicity of Fusarium graminearum on wheat ears
COGEME users meeting - Manchester University November 2005
Online:(http://www.cogeme.man.ac.uk/)


RELATED WORK

General Plant Pathology

Agrios, G. N. 1997. Plant Pathology. Academic Press, Inc., London.

de Bary, H. A. 1879. The Phenomenon of Symbiosis. Strasbourg.

Shaner, G., Stromberg, E. L., Lacy, G. H., Barker, K. R., and Pirone, T. P. 1992. Nomenclature and concepts of pathogenicity and virulence. Annu. Rev. Phytopathol. 30:47-66.


Sequenced Fungal and Oomycete Genomes

Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL. 2006. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313(5791):1261-6.
PMID:16946064

Kamper J, Kahmann R, Bolker M, Ma LJ, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE, Muller O, Perlin MH, Wosten HA, de Vries R, Ruiz-Herrera J, Reynaga-Pena CG, Snetselaar K, McCann M, Perez-Martin J, Feldbrugge M, Basse CW, Steinberg G, Ibeas JI, Holloman W, Guzman P, Farman M, Stajich JE, Sentandreu R, Gonzalez-Prieto JM, Kennell JC, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Munch K, Rossel N, Scherer M, Vranes M, Ladendorf O, Vincon V, Fuchs U, Sandrock B, Meng S, Ho EC, Cahill MJ, Boyce KJ, Klose J, Klosterman SJ, Deelstra HJ, Ortiz-Castellanos L, Li W, Sanchez-Alonso P, Schreier PH, Hauser-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schluter T, Margolis J, Platt D, Swimmer C, Gnirke A, Chen F, Vysotskaia V, Mannhaupt G, Guldener U, Munsterkotter M, Haase D, Oesterheld M, Mewes HW, Mauceli EW, DeCaprio D, Wade CM, Butler J, Young S, Jaffe DB, Calvo S, Nusbaum C, Galagan J, Birren BW. 2006. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444(7115):97-101.
PMID:17080091

Dean, R. A., Talbot, N. J., Ebbole, D. J., Farman, M. L., Mitchell, T. K., et al. 2005. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434:980-6.
PubMed:15846337

Dietrich, F. S., Voegeli, S., Brachat, S., Lerch, A., Gates, K., Steiner, S., Mohr, C., Pohlmann, R., Luedi, P., Choi, S., Wing, R. A., Flavier, A., Gaffney, T. D., and Philippsen, P. 2004. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-7.
PubMed:15001715

Galagan, J. E., Calvo, S. E., Borkovich, K. A., Selker, E. U., Read, N. D., et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859-68.
PubMed:12712197

Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M., Louis, E. J., Mewes, H. W., Murakami, Y., Philippsen, P., Tettelin, H., and Oliver, S. G. 1996. Life with 6000 Genes. Science 274:546-566.
PubMed:8849441

Jones, T., Federspiel, N. A., Chibana, H., Dungan, J., Kalman, S., Magee, B. B., Newport, G., Thorstenson, Y. R., Agabian, N., Magee, P. T., Davis, R. W., and Scherer, S. 2004. The diploid genome sequence of Candida albicans. Proc. Natl. Acad. Sci. U. S. A. 101:7329-7334.
PubMed:15123810

Génolevures 2005. Genomic exploration of the hemiascomycete yeasts.
Online:http://cbi.labri.fr/Genolevures/index.php

Joint Genome Institute 2005. Eukaryotic Genomes.
Online:http://genome.jgi-psf.org/euk_cur1.html

Broad Institute 2005. Fungal Genome Initiative (FGI).
Online:http://www.broad.mit.edu/annotation/fungi/fgi/

Sanger Institute 2005. Fungal genomes.
Online:http://www.sanger.ac.uk/Projects/Fungi/


Reviews on Pathogenicity

Feldbrugge, M., Kamper, J., Steinberg, G., and Kahmann, R. 2004. Regulation of mating and pathogenic development in Ustilago maydis. Curr Opin Microbiol. 7:666-72.
PubMed:15556041

Talbot, NJ 2003. On the trail of a cereal killer: Exploring the biology of Magnaporthe grisea. Annu Rev Microbiol. 57:177-202
PubMed:14527276

Idnurm, A., and Howlett, B. J. 2001. Pathogenicity genes of phytopathogenic fungi. Mol. Plant Pathol. 2:241-255.

Laugé, R., and De Wit, P. J. 1998. Fungal avirulence genes: structure and possible functions. Fungal Genet Biol. 24:285-97.
PubMed:9756710

Knogge, W. 1996. Fungal infections of plants. Plant Cell 8:1711-1722.
PubMed:12239359


Ontologies

Gene-Ontology-Consortium. 2006. The Gene Ontology (GO) project in 2006. Nucl. Acids Res. 34:D322-D326.
PubMed:16381878